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Finds Open Reading Frames (ORFs) = in each supplied nucleotide sequence, stores found regions as annotations.<= /p>
Parameter | Description | Default value |
---|---|---|
Annotate as (required) | Name of the result annotations. | ORF |
Search in | Specifies which strands should be searched: dire= ct, complement or both. | both strands |
Min length | Ignores ORFs shorter than the specified length.<= /td> | 100 |
Genetic code | Specifies which genetic code should be used for = translating the input nucleotide sequence. | The Standard Genetic Code |
Require init codon | Allows or not ORFs starting with any codon other= than terminator. | True |
Require stop codon | Ignores boundary ORFs which last beyound the sea= rch region (i.e. have no stop codon within the range). | False |
Allow alternative codons | Allows ORFs starting with alternative initiation= codons, accordingly to the current translation table. | False |
Parameters in = Workflow File
Type: orf-search
Parameter | Parameter in the GUI | Type |
---|---|---|
result-name | Annotate as | string |
strand | Search in | numeric Available values are:
|
min-length | Min length | numeric |
genetic-code | Genetic code | string Available values are:
|
require-init-codon | Require init codon | boolean |
require-stop-codon | Require stop codon | boolean |
allow-alternative-codons | Allow alternative codons | boolean |
Input/Output Ports= span>
The element has 1 input port:
Name in GUI: Input sequence
Name in Workflow&nbs= p;File: in-sequence
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Sequence | sequence | sequence |
And 1 <= /span>output port:
Name in GUI: ORF annotations
Name in Workflow&nbs= p;File: out-annotations
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Set of annotations | annotations | annotation-table= |